The matchups are going to suck, but just hold up for a bit. In my classic setups, the SWC is either C-USA or the Big 12. The C-USA gets 5+2 bids already. It's not like they won't go to bowl games. And SWC teams have been selected to play in the Liberty Bowl before. Maybe not the champion, but someone still went occasionally. Also like was said, the bowl game is just a game. Half of these didn't even exist 20 years ago so just go with them. It is going to suck in the years after '91, but prior to that, I have the SWC in the Big 12 and put the Big Eight in the Big East. The SEC is also down to 10 teams so I highly doubt they produce 8 bowl eligible teams, or at least that is my hope.
Which this gets me to your next point. If you are making 16 team super conferences, your other conferences are going to be small. Let's say you have 6 16-team conferences. That will leave you with 5 4-5 team conferences. This is probably the extreme, but you are going to see 1, maybe 2 teams each from those small conferences. Who cares if a couple of them squeak through. 5-6 North Texas has also gone to a bowl game as a conference champion. This will open up a ton of at larges to satisfy the teams from the 16-team conferences. The same thing will happen in classic matchups. I've already taken it into consideration in my setups. I already mentioned the Big Eight and SWC. The other conferences were all smaller and did not send many teams to bowl games, like the Big West, MVC, Southland. They are also small conferences, 5-8 teams. No conference will ever use all of their automatic bids. The Big East (Eight) has 6 bids and 8 teams. The Mountain West (PCCA/Big West) has 5 bids and 5-6 teams for the most part. They won't use them all. The SEC has 9 bids and 10 teams. This should open up a ton of bids for independents, or at least that is my hope.
And is bowl prestige even factored in? If you do it the way I do, you lose little prestige. The SWC and Big Eight in the Big 12 and Big East? Seems fine. MVC, Big West, Southland in C-USA, Mountain West, and Sun Belt? And the C-USA and Sun Belt are only used if enough conferences existed, which isn't always true.
If you do go back to pre-1991. Do not send the Big 12 to the BCS and you'll always go to the cotton bowl unless you make the BCS title game. Send the SEC to the Sugar against an at large. Rose is obviously Pac 12 vs. Big Ten. Send the Big East to the Orange to get a Big Eight team in. Leave the rest as at larges. Fiesta took teams from all over the place. Leave 4 at larges and this hopefully gets several independents into the BCS.
So yes, being able to edit all bowl bids is ideal, which means more work. But I'd like to think my setups would accomplish what it is supposed to. Only thing I'd have to check is if my non-1A conferences do what they are supposed to.